Tbp (TATA box binding protein) - Rat Genome Database

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Gene: Tbp (TATA box binding protein) Rattus norvegicus
Analyze
Symbol: Tbp
Name: TATA box binding protein
RGD ID: 67398
Description: Exhibits DNA binding activity. Contributes to RNA polymerase II general transcription initiation factor activity. Involved in positive regulation of transcription, DNA-templated and spermatogenesis. Localizes to transcription factor TFIID complex. Human ortholog(s) of this gene implicated in late onset Parkinson's disease; schizophrenia; spinocerebellar ataxia type 17; and type 1 diabetes mellitus. Orthologous to human TBP (TATA-box binding protein); PARTICIPATES IN cisplatin drug pathway; RNA polymerase I transcription pathway; RNA polymerase II transcription initiation pathway; INTERACTS WITH 2,4-dinitrotoluene; vinclozolin; 1,2-dimethylhydrazine (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: MGC93994; TATA-box-binding protein; TFIID
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,463,330 - 56,480,430 (+)NCBI
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0157,491,381 - 57,509,335 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0158,419,943 - 58,438,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,390,756 - 54,407,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,393,700 - 54,410,507 (+)NCBI
Celera152,668,920 - 52,685,703 (+)NCBICelera
Cytogenetic Map1q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Aoki T, etal., Biochem Biophys Res Commun 1999 Aug 11;261(3):911-6.
2. Chen CM, etal., Schizophr Res. 2005 Oct 15;78(2-3):131-6.
3. Ding T, etal., Cell Mol Neurobiol. 2014 Jul;34(5):669-77. doi: 10.1007/s10571-014-0048-7. Epub 2014 Apr 8.
4. Dumay-Odelot H, etal., Cell Cycle. 2010 Sep 15;9(18):3687-99. Epub 2010 Sep 1.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. GOA data from the GO Consortium
7. Grunberg S and Hahn S, Trends Biochem Sci. 2013 Dec;38(12):603-11. doi: 10.1016/j.tibs.2013.09.002. Epub 2013 Oct 11.
8. Huang S, etal., Brain. 2011 Jul;134(Pt 7):1943-58.
9. Igarashi A, etal., Biochem Biophys Res Commun. 1994 Nov 15;204(3):1125-30.
10. Kelp A, etal., J Neurosci. 2013 May 22;33(21):9068-81. doi: 10.1523/JNEUROSCI.5622-12.2013.
11. Knutson BA and Hahn S, Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):265-73. doi: 10.1016/j.bbagrm.2012.08.003. Epub 2012 Aug 30.
12. Malkowska M, etal., Biochimie. 2013 Apr;95(4):680-91. doi: 10.1016/j.biochi.2012.10.024. Epub 2012 Nov 9.
13. MGD data from the GO Consortium
14. Nakamura K, etal., Hum Mol Genet. 2001 Jul 1;10(14):1441-8.
15. OMIM Disease Annotation Pipeline
16. Owerbach D, etal., Biochem Biophys Res Commun. 2004 Oct 22;323(3):865-9.
17. Payne F, etal., Biochem Biophys Res Commun. 2005 Jun 3;331(2):435-41.
18. Persengiev SP, etal., Mol Endocrinol. 1996 Jun;10(6):742-7.
19. Pipeline to import KEGG annotations from KEGG into RGD
20. Qadri I, etal., Biochim Biophys Acta. 2002 Oct 21;1592(2):193-204.
21. Reid SJ, etal., Brain Res Mol Brain Res. 2004 Jun 18;125(1-2):120-8.
22. Remmers EF, etal., Transplant Proc 1999 May;31(3):1549-54.
23. RGD automated data pipeline
24. RGD automated import pipeline for gene-chemical interactions
25. Sawaguchi T, etal., Early Hum Dev. 2003 Dec;75 Suppl:S109-18.
26. Schmidt EE, etal., J Biol Chem 2003 Feb 21;278(8):6168-74. Epub 2002 Dec 5.
27. Schneider DA Gene. 2012 Feb 10;493(2):176-84. doi: 10.1016/j.gene.2011.08.006. Epub 2011 Aug 26.
28. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
29. Todd RC and Lippard SJ, Metallomics. 2009;1(4):280-91. doi: 10.1039/b907567d.
30. van Roon-Mom WM, etal., Brain Res Mol Brain Res. 2002 Dec 30;109(1-2):1-10.
31. Vannini A Biochim Biophys Acta. 2013 Mar-Apr;1829(3-4):258-64. doi: 10.1016/j.bbagrm.2012.09.009. Epub 2012 Sep 29.
32. Xu Z, etal., Neurotoxicology. 2005 Aug;26(4):729-37.
33. Yogosawa S, etal., Biochem Biophys Res Commun 1996 Dec 13;229(2):612-7.
34. Yoshida T, etal., FEBS Lett 1999 Aug 27;457(2):251-4.
Additional References at PubMed
PMID:7724559   PMID:7729427   PMID:7933101   PMID:8626665   PMID:9027316   PMID:9722567   PMID:9841876   PMID:10526239   PMID:11005381   PMID:11861477   PMID:12411709   PMID:12665565  
PMID:12676957   PMID:14580349   PMID:15601870   PMID:15641800   PMID:15927180   PMID:16263792   PMID:16522640   PMID:16540471   PMID:16822332   PMID:17242199   PMID:17641088   PMID:18218637  
PMID:18722179   PMID:18838386   PMID:19235719   PMID:19861239   PMID:21245044   PMID:22194471   PMID:22323595   PMID:24289924   PMID:25336585   PMID:26638071   PMID:27007846   PMID:27193682  
PMID:27923787   PMID:28134789  


Genomics

Comparative Map Data
Tbp
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2156,463,330 - 56,480,430 (+)NCBI
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0157,491,381 - 57,509,335 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0158,419,943 - 58,438,618 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4154,390,756 - 54,407,563 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1154,393,700 - 54,410,507 (+)NCBI
Celera152,668,920 - 52,685,703 (+)NCBICelera
Cytogenetic Map1q12NCBI
TBP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6170,554,302 - 170,572,870 (+)EnsemblGRCh38hg38GRCh38
GRCh386170,554,369 - 170,572,859 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376170,863,457 - 170,881,947 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366170,705,396 - 170,723,872 (+)NCBINCBI36hg18NCBI36
Build 346170,781,102 - 170,799,578NCBI
Celera6171,658,683 - 171,677,210 (+)NCBI
Cytogenetic Map6q27NCBI
HuRef6168,368,477 - 168,387,004 (+)NCBIHuRef
CHM1_16171,124,696 - 171,144,174 (+)NCBICHM1_1
Tbp
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391715,720,150 - 15,737,689 (+)NCBIGRCm39mm39
GRCm39 Ensembl1715,720,150 - 15,748,641 (+)Ensembl
GRCm381715,499,888 - 15,517,427 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1715,499,888 - 15,528,379 (+)EnsemblGRCm38mm10GRCm38
MGSCv371715,636,852 - 15,654,391 (+)NCBIGRCm37mm9NCBIm37
MGSCv361715,208,038 - 15,221,746 (+)NCBImm8
Celera1716,285,165 - 16,302,716 (+)NCBICelera
Cytogenetic Map17A2NCBI
cM Map178.95NCBI
Tbp
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554113,268,147 - 3,285,077 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554113,268,147 - 3,285,567 (-)NCBIChiLan1.0ChiLan1.0
TBP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16173,800,204 - 173,818,744 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6173,800,240 - 173,826,909 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06168,714,214 - 168,732,744 (+)NCBIMhudiblu_PPA_v0panPan3
TBP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11272,458,959 - 72,479,271 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1272,459,041 - 72,479,124 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1272,221,201 - 72,241,583 (+)NCBI
ROS_Cfam_1.01273,444,412 - 73,464,611 (+)NCBI
UMICH_Zoey_3.11272,717,146 - 72,737,106 (+)NCBI
UNSW_CanFamBas_1.01272,539,334 - 72,559,523 (+)NCBI
UU_Cfam_GSD_1.01272,930,358 - 72,950,554 (+)NCBI
LOC101973510
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946151,203,571 - 151,222,342 (-)NCBI
SpeTri2.0NW_00493709846,572 - 65,304 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.115,669 - 23,675 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
LOC103241044
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11397,661,905 - 97,678,640 (-)NCBI
ChlSab1.1 Ensembl1397,660,864 - 97,681,497 (-)Ensembl
Tbp
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248506,359,382 - 6,375,391 (+)NCBI

Position Markers
Tbp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2156,467,687 - 56,467,977 (+)MAPPER
Rnor_6.0157,495,713 - 57,496,002NCBIRnor6.0
Rnor_5.0158,424,271 - 58,424,560UniSTSRnor5.0
RGSC_v3.4154,394,826 - 54,395,115UniSTSRGSC3.4
Celera152,672,990 - 52,673,279UniSTS
Cytogenetic Map1q12UniSTS
Tbp  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2156,480,048 - 56,480,246 (+)MAPPER
Rnor_6.0157,508,071 - 57,508,268NCBIRnor6.0
Rnor_5.0158,438,183 - 58,438,380UniSTSRnor5.0
Celera152,685,324 - 52,685,521UniSTS
Cytogenetic Map1q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1164407321Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)125439386904217Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1565577285706974Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11131448975844121Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11131448983657083Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11131448983657083Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11131448983657083Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11131448983657083Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11131448983657083Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11249343957493439Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11362925158629251Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12034156058000154Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12107930566079305Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12340642868406428Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)12429779978748000Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13148945479689689Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13444911279449112Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13444911279449112Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13585416780854167Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13585416780854167Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13603316579689689Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13603316579689689Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14190724986907249Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14611346179689689Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14954732883657083Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15052271457861469Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15385134883657083Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15385134883657083Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:64
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000002038
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 26 33 18 19 18 1 1 74 27 41 11 1
Low 17 24 23 23 7 10 8 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002038   ⟹   ENSRNOP00000002038
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl157,491,643 - 57,508,449 (+)Ensembl
RefSeq Acc Id: NM_001004198   ⟹   NP_001004198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,463,618 - 56,480,428 (+)NCBI
Rnor_6.0157,491,643 - 57,508,450 (+)NCBI
Rnor_5.0158,419,943 - 58,438,618 (+)NCBI
RGSC_v3.4154,390,756 - 54,407,563 (+)RGD
Celera152,668,920 - 52,685,703 (+)RGD
Sequence:
RefSeq Acc Id: XM_006227980   ⟹   XP_006228042
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2156,463,330 - 56,480,430 (+)NCBI
Rnor_6.0157,491,381 - 57,509,335 (+)NCBI
Rnor_5.0158,419,943 - 58,438,618 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758747   ⟹   XP_008756969
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0157,491,381 - 57,509,335 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758748   ⟹   XP_008756970
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0157,491,492 - 57,509,335 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001004198 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228042 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81939 (Get FASTA)   NCBI Sequence Viewer  
  EDL99816 (Get FASTA)   NCBI Sequence Viewer  
  EDL99817 (Get FASTA)   NCBI Sequence Viewer  
  EDL99818 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001004198   ⟸   NM_001004198
- UniProtKB: Q66HB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228042   ⟸   XM_006227980
- Peptide Label: isoform X1
- UniProtKB: Q66HB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008756969   ⟸   XM_008758747
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756970   ⟸   XM_008758748
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000002038   ⟸   ENSRNOT00000002038

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13689646
Promoter ID:EPDNEW_R170
Type:single initiation site
Name:Tbp_1
Description:TATA box binding protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0157,491,634 - 57,491,694EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:67398 AgrOrtholog
Ensembl Genes ENSRNOG00000001489 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002038 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002038 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.310.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7115389 IMAGE-MGC_LOAD
InterPro TBP UniProtKB/TrEMBL
  TBP_CS UniProtKB/TrEMBL
  TBP_dom_sf UniProtKB/TrEMBL
  TBP_eukaryotic UniProtKB/TrEMBL
KEGG Report rno:117526 UniProtKB/TrEMBL
MGC_CLONE MGC:93994 IMAGE-MGC_LOAD
NCBI Gene 117526 ENTREZGENE
PANTHER TBP UniProtKB/TrEMBL
Pfam TBP UniProtKB/TrEMBL
PhenoGen Tbp PhenoGen
PRINTS TIFACTORIID UniProtKB/TrEMBL
PROSITE TFIID UniProtKB/TrEMBL
UniProt Q66HB1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tbp  TATA box binding protein      Symbol and Name status set to approved 70586 APPROVED
2001-10-25 Tbp  TATA box binding protein      Name updated 68916 RESERVED

RGD Curation Notes
Note Type Note Reference
gene_function binds specifically to the TATA box promoter element which lies close to the position of transcription initiation 1299882
gene_process plays a role in the activation of eukaryotic genes transcribed by DNA polymerase II 1299882